PLANT OMICs

Encompassing plant and animal OMICs


Agronomic performance of soybean genotypes in Brazil sub-subtropical climate

Gustavo Henrique Demari, Vinícius Jardel Szareski, Ivan Ricardo Carvalho, Valéria Escaio Bubans, José Antonio Gonzalez da Silva, Andrea Bicca Noguez Martins, Leomir Morizzo, Jerffeson Araujo Cavalcante, Ester Mafalda Matter, Devid Araujo Magano, Ítala Thaisa Padilha Dubal, João Roberto Pimentel, Ruddy Alvaro Veliz Escalera, Carlos Eduardo Pedroso, Velci Queiróz de Souza, Tiago Zanatta Aumonde, Tiago Pedó 


Universidade Federal de Pelotas, Capão do Leão, RS, Brasil
Universidade Regional do Noroeste do Estado do Rio Grande do Sul, Ijuí, RS, Brasil
Universidade Federal de Santa Maria, Santa Maria, RS, Brasil
Universidade Federal do Pampa, São Gabriel, RS, Brasil


Abstract
Soybean is the main economic crop of Brazilian agribusiness, and the extreme south of the country is considered a new agricultural frontier. The objective of this study was to evaluate the components of the yield and agronomic performance of soybean genotypes in the south of Rio Grande do Sul as well as to verify the linear relationships of the measured characters. The study was carried out in the municipality of Pelotas, Rio Grande do Sul, Brazil, in the crop harvest 2016. The experimental design was a randomized complete block design, containing 25 soybean genotypes arranged in four replicates. The experimental units were composed of five sowing lines, spaced by 0.45 meters and three meters in length. The measured characters were: first pod insertion height, plant height, number of branches, length of branches, number of pods in the main stem, number of pods in the branches, number of pods with one, two, three and four seeds, contributing to the pod mass with one, two, three and four seeds. The data were submitted to analysis of variance at 5% of probability, where for the significant characters the averages were compared by the Duncan’s test and Pearson's linear correlation was performed in order to identify the tendency of association among the measured characters. The genotypes DM 6159IPRO, BS2606 IPRO, BMX Magna, BMX Potência, TMG7062 IPRO, LG 60163 IPRO revealed superior characters, which can positively influence grain yield. There is a correlation among the morphological characters of the soybean cultivated in southern Brazil between the number of pods in the main stem and the number of pods in the branches, as well as between the number of pods with two seeds and the number of pods in the branches.

Pages 1-6 | Full Text PDF| doi: 10.21475/POJ.13.01.20.p1051
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Estimates of heterosis and combining ability of soybean diallel crossings

Jose Ricardo Bagateli*, Carlos André Bahry, Raimunda Nonata Oliveira da Silva, Ivan Ricardo Carvalho, Giordano Gelain Conte, Francisco Amaral Villela, Gizele Ingrid Gadotti, Geri Eduardo Meneghello

College of Agronomy Eliseu Maciel, Federal University of Pelotas, Pelotas, RS, Brazil
Federal Technological University of Paraná, Dois vizinhos, PR, Brazil


Abstract
This study aimed to estimate the general and specific combining ability of partial soybean diallel crossings. The parents were divided in two groups contrasting for the characteristics of mass of thousand seeds, maturity group, flowers’ color, lodging and growth aspect. The scheme of partial diallel followed the Griffing model, where it were included the parents and the F1 generation. There was predominance of additive genic effects for the characteristics number of seeds per pods, number of seeds per plant and plants height. For number of pods per plant, seeds per plant and mass of hundred seeds the dominance effects were expressed by the superiority of specific combining ability in the determination of these characters. The parents G3 and G7 were the ones that contributed the most to the increase in yield in function of general combining ability for the characters number of pods per plant, seeds per plant, plant yield and mass of hundred seeds. The hybrids from the crossings between G3 x G5 and G3 x G4 are more promising for the characteristics related to yield, since they present elevated heterosis effect and high specific combining ability associated to increase general combining ability presented by the parent G3.

Pages 7-14 | Full Text PDF| doi: 10.21475/POJ.13.01.20.p2038
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NMR-based metabolomics reveals effect of Ganoderma boninense infection on oil palm leaf at 30 days post-infection

Azizul Isha*, Nor Azah Yusof*, Rosiah Osman, Mui-Yun Wong, Siti Nor Akmar Abdullah

Laboratory of Natural Products, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
Functional Devices Laboratory, Institute of Advanced Technology, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
Institute of Plantation Studies, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia


Abstract
Basal stem rot is the major disease in oil palm industry that caused by a fungal named Ganoderma boninense (G. boninense) species. Infected palms are symptomless at the early stage of this disease which imposes difficulties in detecting the disease. Therefore, this study was carried out to obtain the 1H NMR metabolomic profiling of both non-infected and G. boninense infected oil palm leaf at 30 days post-infection (dpi). This combination has provided a rapid approach in investigating the changes in the compound variations of non-infected and G. boninense infected oil palm leaf. Non-infected and G. boninense infected oil palm leaf at 30 dpi was extracted using aqueous methanol (methanol: water, 80: 20 v/v). The crude extracts obtained were analyzed by 1H NMR-based metabolomics approach. Analysis of metabolomics data from 1H NMR was conducted by multivariate data analysis of principal component analysis (PCA). Significant differences were found between the two groups. Compared to the non-infected leaf, the G. boninense infected leaf had higher relative abundance of choline, asparagine, alanine, succinic acid, gallic acid, epicatechin, trimethylamine, N-acetylglucosamine, N-acetyltyrosine, β-sitosterol, 2,3-butanediol, lactic acid, caffeic acid, p-hydroxybenzoic acid, α-tocopherol, β-cryptoxanthin and kaempferol. The non-infected leaf showed higher level of sucrose, xylose, α-glucose, S-sulfocysteine and indole-3-acetic acid. NMR-based metabolomics applied in this study reveals that G. boninense alters a manifold of primary and secondary compounds in oil palm leaf.

Pages 15-20 | Full Text PDF| Supplementary Data PDF| doi: 10.21475/POJ.13.01.20.p2071
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Plant parasitic nematodes occurrence and genetic diversity of banana cultivars grown in Tanzania

Doreen M. Mgonja*, Gladness E. Temu, Sylvester L. Lyantagaye, Abdalah Makaranga, Joseph C. Ndunguru, Nessie D. Luambano

University of Dar es Salaam, College of Natural and Applied Sciences, Molecular Biology and Biotechnology Department, P.O. Box 35179, Dar es Salaam, Tanzania
Tanzania Agricultural Research Institute (TARI)-Mikocheni, Coca cola Road, P. O. Box 6226, Dar es Salaam, Tanzania
TARI-Kibaha, Root and Tuber Section, P.O Box 30031, Kibaha, Tanzania


Abstract
The genetic diversity of bananas (Musa spp.), one of the most economically important crops in Tanzania, is underestimated with scarce reports available. In addition, cultivation of banana is severely constrained by plant parasitic nematodes (PPN). We assessed genetic diversity and population structure of 159 banana varieties from four agro-ecological zones (Northern, Southern highlands, Lake and Zanzibar islands) of Tanzania using 20 SSR markers analysed with UPGMA method. We also, assessed the PPN occurrence through isolation and counting of PPN from each banana genotype where leaf samples were collected. SSR primer pairs were polymorphic; and generated 63 distinct reproducible bands. The polymorphic information content values of each SSR marker ranged from 0.50 to 0.75 indicating high level of genetic diversity among banana varieties. The 159 banana varieties were grouped into two clusters: A and B, based on UPGMA cluster and population structure analysis. A total of 128 independent and 31 overlapping genotypes were identified. Higher kinship among genotypes was observed in cluster A compared with cluster B. Some of the clusters in A and B genotypes showed high genetic distance. The most prevalent and abundant nematode species was Pratylenchus goodeyi with a mean count of 63%, followed by Radopholus similis (31%) and P. coffeae (6%). The results from this study provides a foundation for understanding genetic variability of bananas existing in Tanzania and PPN occurrence that will be valuable information for breeding disease and pest-resistant bananas with high yield traits.

Pages 21-29 | Full Text PDF| Supplementary Data PDF| doi: 10.21475/POJ.13.01.20.p2085
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Application of the LUminometric Methylatoion Assay for plant ecological researches: the study of global DNA methylation in leaves of Elodea canadensis under laboratory conditions and in leaves of fen orchid from wild populations


Natalja Škute*, Marina Savicka, Aleksandrs Petjukevičs, Nadežda Harlamova

Laboratory of Molecular Biology and Genetics, Institute of Life Science and Technology, Daugavpils University, Parades Str.1A, Daugavpils, Latvia

Abstract
The epigenetic changes in the genome of plants are one of the important regulatory mechanisms in response to the environmental factors. The LUminometric Methylation Assay (LUMA) requires a relatively small DNA amount, a short processing time and is easily adapted for species with a non-resolved genome. The LUMA has not been previously used for ecological research of plants. In this research, LUMA was used for the first time to investigate the changes of global DNA methylation under different environmental factors in the leaves of different plants. The influence of salinity on global DNA methylation was studied on aquatic macrophyte Elodea canadensis Michx, which grew in aquatic tanks under different NaCl concentrations. After the third week of growth, the HpaII/MspI ratio was measured by LUMA and global DNA methylation percentages were calculated. The results showed salt stress-induced changes in the global DNA methylation level in E.canadensis leaves, compared to control. The response was salt dose-dependent. The changes of global DNA methylation in wildlife plant populations were analogically assessed on fen orchid Liparis loeselii (L.) Rich. It was shown that global DNA methylation level was higher in leaves of these plants in Engure Lake, where there are temporary changes in water regime, compared to leaves of plants from other places. It was assumed that global GC-DNA methylation plays an essential role in the survival of this plant. Therefore, we show the possibilities of using the LUMA method for epigenetic study of different plants ecological researches.

Pages 30-36 | Full Text PDF| doi: 10.21475/POJ.13.01.20.p2111
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Response of some wheat genotypes to different salinity levels of Irrigated water

Soleman M. Al-Otayk

Department of Plant Production and Protection-College of Agriculture and Veterinary Medicine, Qassim University, Buridah, Qassim, 51452, The Kingdom of Saudi Arabia

Abstract
Salinity is one of the major constraints for crop production across the world. Saudi Arabia is dominated with desert environment with high salinity in the central region of the country. Therefore, salinity has a limiting factor for cereal crops in this region. The objective of this study was to assess the productivity and quality characters for some wheat (Triticum aestivum L) genotypes under different salinity levels of Irrigated water (control, 4000, 8000 ppm NaCl). The experiment was conducted during 2011 and 2012 seasons. The trial was conducted under greenhouse environmental condition at Qassim University Agricultural Research and Experimental Station during 2011 and 2012 seasons. Twenty wheat genotypes including: 5 genotypes from ICARDA, 7 genotypes from Pakistan, 5 Australian genotypes, one American genotype (Yocora Rojo), one Egyptian genotype (Sakha 93) and one local genotype (Sama) were used in this study. Results from wheat genotype trial showed a significant difference (p<0.05) for all traits due to increased salinity in irrigation water from 4000 to 8000 ppm. There was a significant difference between the varieties for plant height, 1000-kernel weight, number of kernels spike-1 and Na for grain and straw. The interaction effect was significant in number of spikes, 1000-kernel weight and Na for grain and hay and Na / K cereal. The results showed that Auqab 2000, Bhan 2000 and Shaka 93 have the highest yield at high level of salt and Sis 13, P2 and Local were the least in yield. Moreover, the results of principle component analysis (PCA) indicated that the superior wheat genotypes for grain yield under salt stress in the two seasons (Auqab 2000, Bhan 2000, Yocara Rojo and Sakha 93) are clustered in group D. These genotypes can be considered as salinity resistant varieties. The maximum reduction over control under salt stress was recorded in Australian genotypes (P6 and P9) and local genotype 'Sama'.

Pages 37-45 | Full Text PDF| doi: 10.21475/POJ.13.01.20.p2268
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Transcriptome analysis of oil palm (Elaeis guineensis Jacq.) roots under waterlogging stress

Sunya Nuanlaong, Suwit Wuthisuthimethavee, Maruay Mekanawakul, Potjamarn Suraninpong*

School of Agricultural technology, Walailak University, Nakhon Si Thammarat, Thailand 80160
School of Science, Walailak University, Nakhon Si Thammarat, Thailand 80160


Abstract
Waterlogging seriously constrains growth and yields in oil palm. To date, the responsive molecular changes caused by waterlogging in oil palm remain elusive. To elucidate the molecular genetic mechanisms of waterlogging stress, two varieties of oil palm Deli x Lamé and Deli x Ghana were used. The transcriptome profiles of the roots under waterlogging stress and normal conditions were compared via Ion Torrent Sequencing. Four libraries (GNR, GSR, SNR, and SSR) of oil palm roots after 45 days of normal watering and waterlogging stress were constructed. Approximately 6.2 million sequenced reads per library were obtained, with 5.5 million mapped reads (88.64%) similar to the oil palm genome in the GenBank database. A comparison of GNR/GSR showed a high of 3,289 DEGs with most genes up-regulated (1,863 DEGs). The GO analysis revealed the distribution of the DEGs among various pathways, suggesting a wide spectrum of physiological processes impacted by waterlogging stress. Moreover, qRT-PCR showed strong expression of all selected RNA-seq genes in waterlogged Deli x Ghana (GSR), especially GST, SAPK10 and NAC29 that are reported for the time to respond to waterlogging stress. Thus, this study not only reveals the comprehensive mechanisms of waterlogging responsive transcription in oil palm, but also establishes Deli x Ghana as a highly-adaptable variety to waterlogging conditions.

Pages 46-56 | Full Text PDF| Supplementray Data PDF| doi: 10.21475/POJ.13.01.20.p2327
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Genome-wide identification of miRNAs targets involved in cold response in cassava

Shuxia Li*, Zhihao Cheng, Ming Peng*

Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China


Abstract
MicroRNAs (miRNAs) are recognized as essential transcriptional or post-transcriptional regulators, and play versatile roles in plants growth, development and stress responses. Cassava (Manihot esculenta) is a major root crop widely grown worldwide. Cold stress seriously affects cassava plants growth, development and yield. MiRNAs and their targets have been extensively studied in model plants, but a genome-wide identification of miRNAs’ targets is still lacking in cassava. In this study, two degradome libraries were constructed using cold-treated and control cassava seedlings to identify the roles of miRNAs and their targets in response to cold stress. Following high-throughput sequencing and comparing with miRNA database, degradome data allowed us to identify a total of 151 non-redundant miRNA-target pairs. We revealed that ~ 42% of miRNA targets are conserved across plant species. However, 83 novel miRNA targets were identified in the two libraries. Gene ontology analyses showed that many target genes involved in cellular and metabolic process. In addition, 12 miRNAs and 31 corresponding targets of them were further found to be involved in cold stress response. Particularly, miR159, 164 and 396 participated in cold stress response by up-regulating certain transcription factors that were involved in the regulation of downstream gene expression. The work helps identifing cold-responsive miRNA targets in cassava and increases the number of novel targets involved in cold stress response. Furthermore, the findings of this study might provide valuable reference and new insights for understanding the functions of miRNA in stress response in plants.

Pages 57-64 | Full Text PDF| doi: 10.21475/POJ.13.01.20.p2337
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Micropropagtion and DNA-barcoding of the endangered endemic Phlomis aurea plant of Saint Katherine

Heba El-Sayed Ghareb, Shafik Darwish Ibrahim, Ghada Abd El-Moneim Hegazi

Tissue Culture Unit, Department of Genetic Resources, Desert Research Center, El-Matareya, Cairo, Egypt
Agricultural Genetic Engineering Institute, Agricultural Research Center, Giza, Egypt


Abstract
Saint Katherine is considered a “biodiversity hotspot” because of the high level of endemism of reported plant species. In this study, conservation of the endangered endemic plant; Phlomis aurea of Saint Katherine, Southern Sinai, Egypt, was carried out through micropropagation and DNA barcoding. The first efficient micropropagation protocol for Phlomis aurea was established as a mean of ex situ conservation of the plant. Shoot tips and nodal segments of in vitro germinated seedlings were established on Murashige and Skoog medium supplemented with 0.54 µM β-naphthalene acetic acid (NAA) and 2.46 µM N6-(2-isopentenyl) adenine (2iP) in combination with 6-benzylaminopurine (BA) or kinetin (Kin). The medium supplemented with 3.48 µM Kin considered optimum for both explants. For multiplication, BA was the most efficient cytokinin. The percentage of rooted explants reached 100% at the concentration of 14.7 µM indolebutyric acid (IBA), whereas the highest number of roots was recorded for 4.90 µM, which considered the optimum concentration with a percentage of 80% of rooting. Rooted plantlets were transplanted in the greenhouse with 75% survival rate. The present study also aimed to carry out DNA barcoding of Phlomis aurea for accurate identification to provide a database for establishing an efficient conservation program for the plant. Three chloroplast DNA markers were used [ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL), maturase K (matK) and RNA polymerase C1 (rpoC1)] and all were successful in amplifying target regions, however the performance of both rbcL and matK markers seemed to be species‐specific. The similarity percentage was maximum for rbcL (99.81%) and matK (100%) compared to the database of the same species.

Pages 65-77 | Full Text PDF| doi: 10.21475/POJ.13.01.20.p2398